nCoV_info

=======================
most longer links here are abbreviated and thus not working
for some full links (without description) see previous post
========================================

 copies of these posts readable also by non-members are here :
https://ncovinfo.createaforum.com/nc...msg239/#msg239
https://www.worldometers.info/coronavirus/#countries
https://ourworldindata.org/grapher/t...hs-per-million
ECDC,varants : https://www.ecdc.europa.eu/en/public...covid-19-eueea
https://www.who.int/emergencies/dise...ronavirus-2019
China : http://www.nhc.gov.cn/yjb/
South Africa : https://gis.nicd.ac.za/portal/apps/o...7606c1248578ff
https://www.nicd.ac.za/diseases-a-z-...datcov-report/
Denmark : https://www.sst.dk/da/corona/tal-og-overvaagning
https://www.sst.dk/en/English/Corona...ics-and-charts
Korea : http://www.cdc.go.kr/index.es?sid=a2
Italy : https://github.com/pcm-dpc/COVID-19/...a-province.csv
https://github.com/pcm-dpc/COVID-19/...ta-regioni.csv

twitter thread about data,dashboards : https://twitter.com/AdamJKucharski/s...40870108569601
Spain : https://www.mscbs.gob.es/profesional...5_COVID-19.pdf
-Fri: https://www.isciii.es/QueHacemos/Ser...sCOVID-19.aspx
Madrid,Wed: https://www.comunidad.madrid/sites/d...anal_covid.pdf
https://www.comunidad.madrid/sites/d...am_covid19.pdf
Aragon : https://transparencia.aragon.es/COVID19
https://www.aragon.es/documents/2012...provincias.csv
Catalunya: https://analisi.transparenciacatalunya.cat/
Russia: https://стопкоронавирус.рф/information/

France: https://www.data.gouv.fr/en/datasets...de-covid-19/#_
https://www.data.gouv.fr/fr/datasets...ques-covid-19/
https://www.data.gouv.fr/fr/datasets...de-covid-19/#_
https://covidtracker.fr/covidtracker...m_medium=email

Germany : https://www.rki.de/DE/Content/InfAZ/...te/Gesamt.html
impf : https://www.rki.de/DE/Content/Infekt...t-Impfung.html
hosp : https://github.com/robert-koch-insti...isierungen.csv


https://www.rki.de/DE/Content/InfAZ/...te/Gesamt.html
https://www.rki.de/DE/Content/InfAZ/...te/Gesamt.html
https://corona.rki.de {no longer works , Oct19}
mobility : https://www.covid-19-mobility.org/current-mobility/
India: https://www.mohfw.gov.in/
https://twitter.com/outbreak_india
Maharashtra : https://www.covid19maharashtragov.in/mh-covid/dashboard
UK dashb. (no longer updated) : https://coronavirus.data.gov.uk/details/cases
ECDC: https://t.co/JZ7VGiITDa?amp=1
ECDC subnational : https://www.ecdc.europa.eu/en/public...-rate-covid-19
ECDC subnational weekly : https://www.ecdc.europa.eu/en/public...-rate-covid-19
ECDC,hosp. : https://www.ecdc.europa.eu/en/public...pancy-covid-19
by age : https://osf.io/43ucn/download
DE: https://www.arcgis.com/sharing/rest/...eb6c7ca74/data
Madrid: https://datos.comunidad.madrid/catal...6-fa97691a2d59

US, by County : https://usafacts.org/visualizations/...-19-spread-map
https://usafacts.org/visualizations/...charles-county
CDC big file (10GB) : https://data.cdc.gov/Case-Surveillan...n8mc-b4w4/data
US,vax by County : https://data.cdc.gov/api/views/8xkx-...sType=DOWNLOAD
Examples
US by State, charts : https://newsnodes.com/us_state/MO
US: R[t] : https://d14wlfuexuxgcm.cloudfront.net/covid/rt.csv
US,deaths : https://data.cdc.gov/api/views/y5bj-...ue% 20target=
USA weekly deaths by cause 2014-2019
https://data.cdc.gov/api/views/3yf8-...ue&format=true
USA provisional deaths 2020-2022
https://data.cdc.gov/api/views/muzy-...ue&format=true
USA deaths by 12quarter,22cause,age+State+ : https://data.cdc.gov/NCHS/NCHS-VSRR-...sele/489q-934x
OxCGRT-Index : https://github.com/OxCGRT/covid-poli...GRT_latest.csv
F,deaths : https://www.insee.fr/fr/statistiques...mmaire=4487854
E,deaths : https://momo.isciii.es/public/momo/data
weekly : https://www.ine.es/jaxiT3/dlgExport.htm?t=35177&L=0

spain ; https://cnecovid.isciii.es/covid19/#ccaa
Belgium : https://t.co/8XtR9D5IKV?amp=1
Vienna : https://coronavirus.wien.gv.at/site/...hlen-aus-wien/
Argentina : https://www.argentina.gob.ar/salud/e.../boletines2020
El Paso : http://epstrong.org/
owid,much data : https://github.com/owid/covid-19-dat...er/public/data
owid,all : https://covid.ourworldindata.org/dat...covid-data.csv


WHO-weekly : https://www.who.int/publications/m
ARD : https://www.tagesschau.de/thema/liveblog/
NDR : https://www.ndr.de/nachrichten/info/
WDR : https://www1.wdr.de/nachrichten/them...s-nrw-100.html
CDS : http://www.worldgovernmentbonds.com/...storical-data/
UK: https://data.london.gov.uk/dataset/c...vid-19--deaths
PHE: https://www.gov.uk/government/statis...llance-reports
London : http://sonorouschocolate.com/covid19...ndonIndicators
Ireland : https://www.gov.ie/en/collection/4b5...ess-briefings/
https://www.hpsc.ie/a-z/respiratory/...%20website.pdf
https://epiforecasts.io/covid/posts/global/

-------------------------------------------------
world , cases+deaths : http://magictour.free.fr/w-0608.GIF
----- update, cases only : http://magictour.free.fr/w-0705.GIF
----- weekly, by cases per pop : http://magictour.free.fr/wo-18.GIF
Italy provinces , cases : http://magictour.free.fr/ip-0531.GIF
France deaths by department : http://magictour.free.fr/F-0406.GIF
France cases : http://magictour.free.fr/ft-0505.GIF
charts for US-States : http://magictour.free.fr/uss0612.GIF
Germany 412 Landkreise : http://magictour.free.fr/lk-0626.GIF
Germany derivative (follows R[t]) : http://magictour.free.fr/de-dv1.GIF
oxcgrt-index : http://magictour.free.fr/oxc2.GIF
UK : http://magictour.free.fr/engl0520.GIF
euromomo : http://magictour.free.fr/eumo21.GIF

--------------------------------
US-Counties with a (2-dose-)vaccination rate of 60% had 40% fewer cases
and 65% fewer deaths
in this delta-wave than Counties with a vaccination rate of 30%

http://magictour.free.fr/coul5g3.GIF


County-cases correlate by -0.17 and deaths by -0.42 with vaccinationrate
http://magictour.free.fr/coulg1.GIF


130000 deaths in USA in this wave so far
I estimate it would have been 250000-400000 without vaccination
and 50000-70000 with Vermont-like vaccination everywhere

going from 40% fully vaxed to 50% fully vaxed gave a reduction in 18% of cases
and 35% of deaths in this wave for an average US-County.
Or (fully) vaxing 700 US people saved one life in this wave

c
Last edited by gsgs; 10-25-2022 at 08:23 AM.

Italy update :
https://www.epicentro.iss.it/coronavirus/bollettino/Bollettino-sorveglianza-integrata-COVID-19_31-maggio-2022.pdf

reinfections back to 6% (figura 21)

VE(3dose; case,hosp,ICU,death) now at 08,70,74,84
,10 weeks ago it was 48,86,91,93

case , 27,08,22, 00,00,00, 44,46,55
hosp , 54,28,38, 66,58,58, 82,80,72
ICU  , 67,47,41, 74,71,50, 84,86,74
death, 58,27,51, 72,76,78, 89,88,87

VE in % in France during the omicron wave , 2022-12-13 - 2022-05-22
numbers estimated from the graphics at
https://drees.solidarites-sante.gouv.fr/communique-de-presse/statut-vaccinale-des-personnes-testees-ou-hospitalisees-avec-covid-19-derriere


2dose , 3dose>3m , 3dose<3m ; 40-59,60-79,80+

average of the 3 agegroups :

        2,3>,3<
---------------
case , 19,00,48
hosp , 40,61,78
ICU  , 52,65,81
death, 45,75,88

basic vaccinations (2dose) seem to play a bigger role wrt. deaths than boosters
almost no effect on case-counts  (urban USA, omicron-wave)
http://magictour.free.fr/cou23a.GIF
550 Counties with population >100000, making 71% of the US-population
(also excluding the big rural.urban differences of omicron)
taking % of elderly boosted (19%-94%, omitting 9 Counties with extreme values,
and some Sates not available, e.g. Florida)
average of Counties, not weighted by population
(focussing on County policy , no magnitude-bias)
gives deathrates
49,60,60,69,60,64,59,62,50,40
for 0-10%,...,90%-100% of elderly boosted (average of 2 values in Dec.and Feb),
I forgot the exact dates)
cases and deaths from usafacts, vax from CDC)

(processed) datafiles :
cou23a.r1
cou23b.r1
result-file : cou23.l2

update 2020


monthly deaths USA 1959-2020 : http://magictour.free.fr/1959m.GIF

by 30 causes since 1969 : http://magictour.free.fr/tot30.GIF

COVID got an extra code : U07.1 , which is not included in any of the 30, except "all" and age45-54

monthly deaths from U07.1 in 2020 in USA :
3+16+6773+61950+35254+15812+28264+27011+16842+2206 8+48004+89533 = 351530
total deaths in 2020 :3390278 after 2861523 in 2019 , +528755


excess mortality by age  http://magictour.free.fr/ :  http://magictour.free.fr/x2020m.GIF

it's 20% and almost constant (age)  (except <10y) ,
2%-10% higher for males, dependding on age

actual omicron vaccine effectiveness reports
-------------------------------------

location,date,doses,time since last dose, VE(case,symp,hosp,ICU,death)


UK-:40,--,93          waning by 2% and 1.2% per week
DEU:--,75,90,96,96    clinical symptoms
ITA:--,68,  91
ICE:42,--,80
ISR:40,--,88
ONT:15,--,50     2-3 dose
-NY:--,77,92
-CA:87,--,93
-OR:83,--   2dose:68,--
-WA:75,86     2-3 dose
FRA:--,88,86,--           1201-0116         -27(00-19)
FRA:--,69,79,--
FRA,2021-12-12,:86,91,93,96,90           case,symp,hosp,ICU,death  age>20

scroll down for the most actual numbers

actual numbers on hospitalisations and positive-rates here:
https://ncovinfo.createaforum.com/genetics/b-1-1-529-(nu-)/msg320/#msg320

: https://ourworldindata.org/grapher/united-states-rates-of-covid-19-deaths-by-vaccination-status


https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1044481/Technical-Briefing-31-Dec-2021-Omicron_severity_update.pdf

UK,symp,  http://magictour.free.fr/tb34a.GIF
UK,hosp:
VE(UK,h,1d, 7w,O)=52
VE(UK,h,2d,11w,O)=72
VE(UK,h,2d,30w,O)=52
VE(UK,h,3d, 4w,O)=88



Ontario , VE(case),1129-1231
76,76,74,74,72,73,72
71,70,69,67,67,64,63
59,53,47,40,32,25,16
+08,+01,-05,-12,-18,-25,-28
-31,-33,-29,-32,-38

Ontario , VE(hosp),1213-1231
84,84,83,82,82,81,81
79,78,77,75,73,70,66
63,60,56,54,47






---------------------------------------------------------
Robert Koch Institute report released today states that 95.58% of the #Omicron cases
in Germany are fully vaccinated (28% of those had a "booster"), 4.42% are unvaccinated.
--------------------------------------------------------
 the 2nd dose mRNA vaccine given to someone who also had past infection
did not further increase antibodies
---------------------------------------------------
> One of the studies shows omicron is 89% as severe in people with no vax, never infected
------------------------------------------------------


vaccine effectiveness

AZ,BNT,Mod
D,2,h,78,91
D,3,h,98,98
O,2,h,51,75
O,3,h,90,86
O,2,h,ar,54,77
O,3,h,ar,92,88


O,2,s,--,55,37

ar:adjusted for reinfections
s: symptomatic disease
h:hospitalisation
O:omicron
D:delta
w:weeks

https://twitter.com/freja_kirsebom/status/1474070653326270473

O,2AZ+BNT,s,3w,60
O,2AZ+BNT,s,10w,35
O,2AZ+Mod,s,10w,45
O,3BNT,s,1w,70
O,3BNT,s,10w,45
O,2BNT+Mod,9w,72
O,2Mod,3w,50
O,2Mod,22w,0

---------------------------------------------------------------------------

DNK,VE : https://www.medrxiv.org/content/10.1101/2021.12.20.21267966v2.full.pdf

---------------------------------------------------------------------

VE(3*BNT,omicron,symp)=75%
-----------------------------------------------------------------
SinoVac doesn’t provide sufficient antibodies to neutralize omicron
------------------------------------------------------
VE(2xBNT,omicron,hosp)=70%
VE(2xBNT,omicron,inf)=33%

wanes
1. 2-4 wks after 2nd dose: 56%
2. 3-4 mnths after 2nd dose: 25%

VE(delta-->omicron,inf)=60%
----------------------------------------------------------------
VE(symp,2AZ,omicron,5m?,UK)=0
VE(symp,2BNT,omicron,5m?,UK)~30%
VE(symp,3BNT,omicron,1m,UK)=72%
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1040076/Technical_Briefing_31.pdf
https://twitter.com/kallmemeg/status/1469351833416122369
------------------------------------------------
current vaccine effectivity in Iceland
see  https://www.covid.is/data
VE(2shots,case) = -88% (Jan02)
VE(3shots,case) = 38% (Jan02)
VE(2shots,hosp) = 71% (Dec28)
VE(3shots,hosp) = 84% (Dec28)
------------------------------------------------


Iceland : http://magictour.free.fr/ice1228.GIF
VE(ICE,case,3d,5w,O)=48
VE(ICE,case,2d,20w,O)=-82%

Washington : http://magictour.free.fr/wa-1229.GIF
VE(WA,case,omicron)=60%

New York : http://magictour.free.fr/ny-1222.GIF
VE(NY,case,omicron)=75

Virginia : http://magictour.free.fr/va-1225.GIF 
VE(VA,case,omicron)=92%

UK,symp,  http://magictour.free.fr/tb34a.GIF

Ontario :  VE(case)= -31%  VE(hosp)=45% , VE(ICU)=84%    (was 73%,82%,90% 5  weeks ago)
http://magictour.free.fr/ont-0105.GIF

California : VE(case)=75% (-1% per day) , VE(hosp)=87% (-0.5% per day)  , VE(death)=95% (stable)
http://magictour.free.fr/ca-1226.GIF

Oregon, Dec30 : http://magictour.free.fr/or-1230.GIF
VE(case)=66%

Germany, Jan06 : http://magictour.free.fr/rki2w01.GIF
VE(case,2dose,18-59)= 53 , VE(hosp,18-59)=76  , VE(ICU)=89
VE(case,3dose,18-59) = 82 , VE(hosp,3dose,18-59)=92
(it's for the last 4 weeks , still mostly delta, the omicron wave is just starting,
mainly young people get it early in the wave, so I took 18-59 and not 60+)
----------------------------------------
USA-CA :
VE(Mod,case,O,2dose,14-90d)=30    quickly declining
VE(Mod,case,O,3dose,)=63
https://www.medrxiv.org/content/10.1101/2022.01.07.22268919v1
----------------------------------------

vaccine effectiveness in UK with 2-3 doses ,
4-week average
average of 4-5 highest from 7 agegroups
ONS-denumerators
reported in weeks 1,2 of 2022

VE(case) , av(5)=26.1% , 22.8%
VE(admis) , av(5)=+91.5%  ,  +89.1%
VE(death) , av(4)=+92.4% , +93.2%

-----------------------------------------------------------
VE-numbers in % for case/symp , hosp , ICU , death

ONT,0112 , VE(2+dose)=-25,40,77,--

ICE,0105 , VE(2dose) = 00,66,--,--
ICE,0105 , VE(3dose) = 32,68,--,--

Germany actual estimates from 4-week-period-numbers
DEU,0113 , VE(2dose) = 00,59,76,82
DEU,0113 , VE(3dose) = 40,83,86,89

----------------------------------------------------------------
Italy :
https://www.epicentro.iss.it/coronavirus/bollettino/Bollettino-sorveglianza-integrata-COVID-19_12-gennaio-2022.pdf

fig.A10,A11
VE much better in old people ? I assume it's because omicron infects young people first
 and the VE(old) will go down to the VE(young) in some weeks

Ontario, 01-25  : http://magictour.free.fr/ont-0125.GIF
VE(2+dose,case)=15%    , VE(2+dose,hosp)=50%   VE(2+dose,ICU)=80%
but these are lower numbers in the decreasing wave , VE was lower at the peak of the wave

DE : 2d:30,55,90,90  ;  3d : 65,84,90,90   (symp,hosp,ICU,death)
http://magictour.free.fr/rki2-w03.GIF

ITA : 2dl : 08,84 ; 2ds : 31,89 ; 3d : 46,94    (case,severe case) 2d >/< 120days ago

Iceland , VE(3dose,case) = 40% , VE(3dose,hosp) = 65%

California :VE(case)= 76% , VE(hosp) = 85% , VE(death) = 95%
http://magictour.free.fr/ca-0109.GIF

New York City : VE(case)=60% , VE(hosp)=88%
(NY-State gives 78% and 92%)
http://magictour.free.fr/nyc-21.GIF

France , 2022-01-01 , 2dose : -25% , 57% , 72%  (case,hosp,ICU)
France , 2022-01-01 , 3dose :  48% , 74% , 85%  (case,hosp,ICU)

Iceland, 2022-01-25  :  VE(2dose,case)=-35% , VE(2dose,hosp)=60% ,
VE(3dose,case)=40% , VE(3dose,hosp)=80%
http://magictour.free.fr/ice-0125.GIF

Germany, 2022-01-27 , http://rki2w04.GIF    40,70,80,85   ,   75,90,96,94

Israel, 2022-01-27 , average of 5 oldest age10groups
2dose>6m : 45,63 ; 2d>6m or 3dose : 45,88     for inf.,severe

UK,3dose : http://magictour.free.fr/3dosek.GiF

2022-01-16 , California : http://magictour.free.fr/ca-0116.GIF
68,80,87,93   2,3dose ; case,hosp


( how can it be 76% in CA and NY  but 10% in ONT and 40% in ICE ? )
46 in ITA , 30 in UK , 70% in DE


s also the effect that unvaccinated people are more likely to have natural immunity
and this increasing over time. Countries/States rarely report cases nd hospitalisations by
vaccination status _and_ status of previous infection

early omicron severety studies :

ZAF : https://t.co/g24KTGU7Io
DNK : https://t.co/pQnetTf7IP
ENG : https://t.co/chqPEhph3p
SCO : https://t.co/CMv2zkG2sh

DNK,VE : https://www.medrxiv.org/content/10.1101/2021.12.20.21267966v2.full.pdf


-------------------------------------------------------------------------
vaccine effectiveness

AZ,BNT,Mod
D,2,h,78,91
D,3,h,98,98
O,2,h,51,75
O,3,h,90,86
O,2,h,ar,54,77
O,3,h,ar,92,88


O,2,s,--,55,37

ar:adjusted for reinfections
s: symptomatic disease
h:hospitalisation
O:omicron
D:delta
w:weeks

https://twitter.com/freja_kirsebom/status/1474070653326270473

O,2AZ+BNT,s,3w,60
O,2AZ+BNT,s,10w,35
O,2AZ+Mod,s,10w,45
O,3BNT,s,1w,70
O,3BNT,s,10w,45
O,2BNT+Mod,9w,72
O,2Mod,3w,50
O,2Mod,22w,0

-------------------------------------------------------------------------
=============================================
 SARS CoV-2 entry into a cell can occur via two routes: one that only needs ACE2 and
another that needs ACE2 and TMPRSS2.
TMPRSS2 (T2) is higher in the lower airways and so virus goes the second route in those areas.
Omicron spike has reduced ability to use the ACE2+T2 route and doesn't respond to higher
T2 levels, unlike Delta
==========================================================

TB33 : risk(EC or hosp,omicron)=0.62*risk(EC,delta)
risk(hosp,omicron)=0.38*risk(hosp,delta)
This effect is still present when stratified by vaccination status

Using a very similar data set, Imperial College, provided estimates that Omicron cases had a 15
to 25% (Hazard ratio 0.8; 95% CI 0.75-85) reduced risk of emergency department attendance
(hospitalisations in their data set) and 40 to 49% (HR 0.55, 95% CI 0.51-59) reduced risk of a
hospitalisation with a stay of one or more nights. Importantly, this group attempt to impute the
effect of prior infection, highlighting that while 17% of the population have tested positive for
COVID-19, this is likely to capture only one-third of total infections that have occurred in
England. Including the likelihood of previous infection, in addition to vaccination in their model,
they have estimated the intrinsic risk difference between Delta and Omicron as between 0 to
30% and the reduced risk of hospitalisation in those previously infected estimated as 55 to 70%.
===========================================================
The Sato Lab (Kei Sato)  @SystemsVirology
Japan - #Omicron is less infectious and pathogenic than #Delta and even an early pandemic
SARS-CoV-2 in infected hamster model. 1/5
-----------------------------------------------
Omicron infection enhances neutralizing immunity against Delta
------------------------------------------------
> One of the studies shows omicron is 89% as severe in people with no vax, never infected
-----------------------------------------------------------------
Coetzee :
"And their symptoms don't seem to get any worse than that. After about five
days they clear up, and that's it."
-------------------------------------------------------------------------
Omicron appears to have switched cell entry preference to endosomal fusion
(rather than ACE2+TMPRSS2 mediated cell surface fusion
like previous variants, incl. the well adapted Delta)
----------------------------------------------------------------------
Robert Koch Institute report released today states that 95.58% of the #Omicron cases
in Germany are fully vaccinated (28% of those had a "booster"), 4.42% are unvaccinated.
--------------------------------------------------------
 the 2nd dose mRNA vaccine given to someone who also had past infection
did not further increase antibodies
---------------------------------------------------
---------------------------------------------------------------
    Daily modelled estimates produced by the ONS showed around 9.5% of Londoners had
COVID-19 as of Sunday
    Report also showed a record 1 in 35 people in England had COVID-19 between Dec.
13 and Dec. 19
The ONS report also showed a record 1 in 35 people in England had COVID-19 between Dec. 13 and Dec. 19 — compared with a previous estimate published on Thursday of 1 in 45 in the week to Dec. 16.
7% infected in London during Christmas
-----------------------------------------------------------------
Study estimates nation’s Omicron outbreak grew 70% in a week to hit one in 25 people – as data shows infections are now rising quickest in over-65s

The Office for National Statistics swabbing estimates that 2.03 million people had the virus
on any given day in the week before Christmas
2022-01-01 , granthshala.com
The ONS conducts weekly surveillance tests
----------------------------------------------------------------------
2022-01-04 , Neil Ferguson warns of 5,000 Omicron deaths a DAY in UK
ahh, seems to be old news (I had missed it)
Published: 15:38 GMT, 17 December 2021 | Updated: 23:58 GMT, 17 December 2021
---------------------------------------------------------------------
@IHME_UW
 new projections show that daily estimated #COVID19 infections has peaked at 6.2 million
on 1/6 in the US, but daily cases will rise to nearly 1.2 million by 1/19, 2022.
80-90% asymptomatic
---------------------------------------------------------------
intrinsically reduced virulence may account for an approx 25%